Question: Adapter and quality trimming using Trim Galore integrated Galaxy
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gravatar for evensky.maria
24 months ago by
evensky.maria0 wrote:

Hello. I need to make adapter trimming and quality trimming for my FASTQ paired files. I work in the operating system Windows 8 thats why I decided to do it using Trim Galore in GALAXY. I registered here https://usegalaxy.org and I choosed "NGS: QC and manipulation" -> "Trim Galore". But how to proceed, I can't understand. Please tell me. It requires downloading files (possibly, gz-archives)? but they are of great size.

Kind regards, Maria.

ADD COMMENTlink modified 24 months ago by Jennifer Hillman Jackson25k • written 24 months ago by evensky.maria0
0
gravatar for Jennifer Hillman Jackson
24 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

Inputs to the tool can be uploaded, even large files (up to 50 GB). Use the FTP method defined here: https://wiki.galaxyproject.org/Support#Loading_data

Fastq data should be properly prepared and have the correct "datatype" assignment. This is how: https://wiki.galaxyproject.org/Support#FASTQ_Datatype_QA

More about NGS data in general is covered in detail in this tutorial: https://github.com/nekrut/galaxy/wiki/Introduction-to-NGS-technologies

For usage, the underlying tool binary's manual (linked from the tool form) defines the tool functions. The wrapped Galaxy tool implements most of these.

After reviewing, if there is a specific option/function you are not sure about, we can help.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 24 months ago by Jennifer Hillman Jackson25k

hi jen i request you to please elaborate on trimming by using trimmomatic. i am working on single end NGS data. i got 60 percent mapping after trimming by trim galore so wanted to switch over to some other trimming method for improving the mapping. i requet you to pleae guide me and help me to do the same. i have read the paper also on trimmomatic. but what exactly parameters i should set i request you to help. thanks

ADD REPLYlink written 21 months ago by 1603.neha70
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